PLA Release Notes
=================

Release v500 (PL-Model of Mar 8, 2006)
------------

+ "Compare" functionality: A new menu allows to select other, currently open networks to compare the frontmost one to.

+ New button "Show Info" for node context menu (which is also default action upon double-click); double-clicking on nodes now does the following:
  Rule: show rule in Maude code
  Occ: show info (see above)

+ Finding complexes:
    sorting new complexes in list of occs ignoring special characters '(', ':', ')' so that, e.g., "(Ikb:(Nfkb1:Rela))-CLc" would appear between "Ifnggene-on- NUc" and "Ikb-degraded-CLc"
    also made the auto-completion in finding occs now break up the complexes (again using special characters '(', ':', ')') so that typing "eif" and possibly hitting TAB to cycle through will eventually highlight somthing like "(4Ebp1:Eif4e)-CLc"

+ Bulk selection tool for goals, avoids, and hide-rules.  A new (albeit small) button "In Bulk..." appears for each setting at the top of the tree in the GUI view.  Clicking it opens a new dialog with an editable text area, into which the user can enter (or copy-and-paste) a list of chatty labels.  There is also a "File..." button that lets the user choose a file to read the contents from.  The file contents will be displayed in the text area.  Finally, a check box lets the user NEGATE the selection made in the text area: if checked, only items in the tree that DO NOT match will be selected.  Any current selection remains untouched (so use Reset All or All Off first to clear things out).  Also, in case of contradicting selections (e.g., goals and avoids), the currently disabled items will not be altered.

+ Graph ID is now displayed in title of frames

+ "Show Subgraph" functionality:  Generate and display a subgraph from a list of given node names (chatty labels or long names).  The new subgraph contains all named occurrences and rules.  For each rule, all incoming and outgoing occurrences will appear in new subgraph as well.


Release v459
------------

+ PLA Additional functionality
     show maude rule now works
     you can export a network as sbml or ad hoc but simple pn format
     (for now this must be done from the IOP gui,
       see end of input.txt in new model for sample commands)
     If you have created a subnet for some goal(s) you can as for
     the single knockouts to be listed -- also must be done from
     the IOP gui using the displayKOSs command.  To find the
     graph name to use as argument do <cmd>I / <ctl>I in the graph window.
    
+ PL a new function has been added to theops.maude (reduce)
     You will need to use the new model (PL-v459.zip)
     or copy the definition of reduce into your theops.maude
     for display of networks to work